On your next cvs update it may look like I've made sweeping changes, but that's not really the case.
Fixed all Javadoc warnings/errors on 1.4, general Javadoc cleaning Fixed a couple of things which turned up in a grep for 'fixme' Enhanced RestrictionEnzyme and RestrictionEnzymeManager. Added a RestrictionSite feature. This involved pulling RestrictionEnzyme back into the main code tree (it was in src-1.4) because I added SimpleRestrictionSite to the default FeatureRealizer. (Adding to the default FeatureRealizer seems to be the approach used most often). Added RestrictionMapper which implements SequenceAnnotator for marking RestrictionSite features on a Sequence by creating a ViewSequence. The searching is configurably multithreaded via a basic thread pool interface. This class is not unit tested yet - only by visual inspection of annotated EMBL dumps. As you might expect, it's only about 30-40% of the speed of EMBOSS restrict (by highly accurate wristwatch benchmarking... ). However, I guess native threads on a multi-cpu machine will close the gap. Keith -- - Keith James <[EMAIL PROTECTED]> bioinformatics programming support - - Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK - _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
